University Of British Columbia

Sep 26 and 28, 2017

12:00 pm - 7:00 pm

Instructors:
Alex Razoumov

Helpers:
Kim Dill-McFarland

General Information

Software Carpentry
aims to help researchers get their work done
in less time and with less pain
by teaching them basic research computing skills.
This hands-on workshop will cover basic concepts and tools,
including program design, version control, data management,
and task automation.
Participants will be encouraged to help one another
and to apply what they have learned to their own research problems.

Requirements: Participants must bring a laptop with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges
on. They should have a few specific software packages installed (listed
below). They are also required to abide by
Software Carpentry's
Code of Conduct.

Windows

Keep "Use Git from the Windows Command Prompt" selected and click on "Next".
If you forgot to do this programs that you need for the workshop will not work properly.
If this happens rerun the installer and select the appropriate option.

If your "HOME" environment variable is not set (or you don't know what this is):

Open command prompt (Open Start Menu then type cmd and press [Enter])

Type the following line into the command prompt window exactly as shown:

setx HOME "%USERPROFILE%"

Press [Enter], you should see SUCCESS: Specified value was saved.

Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

The default shell in all versions of Mac OS X is Bash, so no
need to install anything. You access Bash from the Terminal
(found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep
Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing bash. There is no need to
install anything.

Git

Git is a version control system that lets you track who made changes
to what when and has options for easily updating a shared or public
version of your code
on github.com. You will need a
supported
web browser (current versions of Chrome, Firefox or Safari,
or Internet Explorer version 9 or above).

You will need an account at github.com
for parts of the Git lesson. Basic GitHub accounts are free. We encourage
you to create a GitHub account if you don't have one already.
Please consider what personal information you'd like to reveal. For
example, you may want to review these
instructions
for keeping your email address private provided at GitHub.

Windows

Git should be installed on your computer as part of your Bash
install (described above).

Mac OS X

For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
After installing Git, there will not be anything in your /Applications folder,
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.

Linux

If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo yum install git.

Text Editor

When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on Mac OS X and
Linux is usually set to Vim, which is not famous for being
intuitive. if you accidentally find yourself stuck in it, try
typing the escape key, followed by :q! (colon, lower-case 'q',
exclamation mark), then hitting Return to return to the shell.

Windows

nano is a basic editor and the default that instructors use in the workshop.
To install it,
download the
Software Carpentry
Windows installer
and double click on the file to run it.
This installer requires an active internet connection.

Others editors that you can use are
Notepad++ or
Sublime Text.
Be aware that you must
add its installation directory to your system path.
Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop.
See the Git installation video tutorial
for an example on how to open nano.
It should be pre-installed.

Linux

Python

Python is a popular language for
research computing, and great for general-purpose programming as
well. Installing all of its research packages individually can be
a bit difficult, so we recommend
Anaconda,
an all-in-one installer.

Regardless of how you choose to install it,
please make sure you install Python version 3.x
(e.g., 3.4 is fine).

We will teach Python using the IPython notebook, a programming environment
that runs in a web browser. For this to work you will need a reasonably
up-to-date browser. The current versions of the Chrome, Safari and
Firefox browsers are all
supported
(some older browsers, including Internet Explorer version 9
and below, are not).

Linux

Download the Python 3 installer for Linux.
(Installation requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)

Open a terminal window.

Type

bash Anaconda3-

and then press
tab. The name of the file you just downloaded should
appear. If it does not, navigate to the folder where you
downloaded the file, for example with:

cd Downloads

Then, try again.

Press enter. You will follow the text-only prompts. To move through
the text, press the space key. Type yes and
press enter to approve the license. Press enter to approve the
default location for the files. Type yes and
press enter to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).